Coming Home
by lonelyinthesky
Summary: Post season 4 finale. Michael wakes up in Company Headquarters, only to discover he has been in their clutches for months now. When everyone that Michael cares for is threatened, Michael is forced to work for the very organization that ruined his life. Will he find a way to escape, as he has so often in the past? Or will he accept his fate, and stay in Company clutches forever?
1. Chapter 1: The Beginning

**A/N: Hello all! This is my very first story, so please bare with me. I know this idea has been done thousands of times, but I hope you enjoy my take on my dream ending of Prison Break!**

**Disclaimer: I don not own Prison Break or any of the characters (because if I did the ending would have been a little bit more like this).**

**This story has not been beta'ed, so all mistakes are mine!**

Chapter 1: The Beginning

His eyes snapped open. Was this what heaven was like? It wasn't quite how he imagined. For one, there was far too much grey, and nowhere near enough light. When his eyes finally refocused and adjusted to the too bright lights, he realized that this wasn't heaven. This wasn't heaven at all. As he became more and more alert, he realized that his surroundings were all too familiar. Yes, he knew exactly where he was and it was nowhere near what heaven should be. Not the place he always dreamed of: on a beach somewhere with Sara in his arms and a beer in his hand. No, this place was no heaven. It was hell. He sat up and finally completely took in his surroundings. He had somehow been captured by the Company. It was the only explanation. How else could he have ended up in the same room in which Company doctors performed his life saving tumor removal surgery? He almost couldn't believe it. In fact, if it weren't for the doctor poking and prodding him and the businessman dressed in suit walking toward him with a smile on his face, he wouldn't have.

"Ah, finally. Welcome back, Mr. Scofield," the man in the suit greeted as the doctor left the room abruptly.

"What am I doing here? I thought we had already taken down the Company once."

"Yes indeed it would appear that way, but General Krantz has always had a backup plan. He figured one day someone would come along and 'take him and the Company down', he just never assumed that day would come so quickly. He also never assumed the ones to do it would be a group of ex-cons, a crook for a homeland security officer, and a pretty doctor. What's her name again? Is it Sara? Such a lovely girl. From what my men have been telling me, pregnancy is treating her well. She really has such a glow about her, if you know what I mean."

At the mention of Sara, Michael leaped into action. Before he knew it he had his hands on the man's collar and was pinning him up against the wall. "Don't touch her!" he snarled. "If you touch her I swear to God I'll–"

"You'll what, Mr. Scofield," the man interrupted. "There's not much you can do seeing as outside these doors there are two guards with guns and believe me, are not afraid to use them. As much as I value the mind of the son of Christina Scofield, those men do not, and they believe that all minds are replaceable. I however see things differently. Now if you'll calm down and let me go, we can work out an arrangement."

Michael released the man to the ground. "Just don't hurt them, please," he pleaded with desperation evident in his voice.

"Oh Mr. Scofield," the man started, "that is the last thing that I want to do. Now I'm sure you have many, many questions, so I'll start from the beginning, but first, allow me to introduce myself. My name is Jeremy Krantz, and the General, the very man who you sent to prison, is my father."

**So there's the first chapter. I know it's short, but it's a start! Thanks for reading!**


	2. Chapter 2: The Expanation

Chapter 2: The Explanation

"I'm sorry, what?! I didn't even know the General had a son!" Michael exclaimed as he slowly made his way back to his bed to sit down. He wasn't feeling that great, and his legs felt far too weak. How long had he been asleep? And more importantly, how long had the new Company had him in their clutches?

"No one, outside of my mother and my sister Lisa, did. Growing up, I took my mother's maiden name and became Jeremy Stevens," Jeremy explained as he walked toward where Michael was sitting. "I was only four when my parents got divorced, and while my sister Lisa went to live with my father, I went to live with my mother. However my mother died months after my eighteenth birthday, and my father convinced me to join him, and be his right hand man in the matters of Company business. I have observed his every move for the past several years."

"But how is that even possible? No one has ever even heard of you?"

"Well you see Mr. Scofield," Jeremy began, "I have been kind of a behind the scenes man. I am and have been for the past 15 or so years my father's 'backup plan'. He knew he wasn't bullet proof, and would one day no longer be a part of the Company. It was always a part of the plan that I would become the head of the Company when my father was no longer in the picture. Not only have I been watching you, your family, I have also worked side by side with Christina, may she rest in peace. I admired her work greatly. Now I'm sure you're wondering how I managed to obtain the power, connections, and plans necessary to recreate an organization as powerful as the Company, and the truth is that the Company never ended. Yes we lost Scylla, and yes my father is on death row, but we had far more plans beyond Scylla, and far more connections than my father. Under my leadership, the Company has regained almost all of its influence in just these past seven months."

_Seven months, _Michael thought. _How could I possibly have been in a coma for seven months?! Sara must be due any day now._ Rather than voicing his thoughts to Jeremy, Michael instead asked, "How did I get here? And why have I been in a coma for so long?"

"Well you see Michael, can I call you Michael?" Jeremy started, "When our inside contacts received you from the lovely Miami-Dade Penitentiary for Women, you were in pretty bad shape; and by 'pretty bad shape' I mean you were dead and your heart had to be shocked back to life with a crash cart. Alas the Company doctors were able to revive you, and ran some run-of-the-mill scans to see how much damage the electric shock you suffered from did. It was during these scans that they discovered your tumor had once again returned. You were rushed into surgery, where the doctors successfully removed your tumor. However the surgeries and near death-experiences really took a toll on your body, thus you fell into a seven month coma."

For the first time since he woke, something made sense. He realized that the headaches that he had become so accustomed to for the past year of his life, were gone, and for that he was grateful. "Why did you try so hard to bring me back? I mean from the sound of it, it sounds like you may have been better off to just leave me to die."

"Your mind is so valuable to us. It is a vital instrument for the Company to have in order to rebuild itself. Your mother helped build the Company and its operations. It is largely because of her that the Company became the success that it was. And from what I've been told you are as brilliant, if not more, than she was. We need you to help us rebuild the Company. So what do you say? Partners?"

As much as Michael wanted to scream "ARE YOU OUT OF YOUR FREAKING MIND?" he restrained himself. He knew he had to be smart in this situation because due to his lack of weapons as well as weak physical state, he knew there was no way he could win this fight. If he wanted the chance of ever seeing his family again, he'd have to be smart. "What if I say no?" Michael tested.

"Ah I was afraid you wouldn't see the benefits of creating a new and improved Company. So I've decided to create a little bit of inspiration."

Suddenly, Jeremy turned on the screen in the front of the room. Michael's eyes went wide as he was horrified by the picture in front of him. It was a split screen showing live surveillance of not only Sara, but Lincoln and LJ as well.

"I have men close by at all times. If you make one wrong move, Sara might accidently end up in a multi-car accident, or Lincoln may get into a bar fight with a man who may or may not be armed. It's these kinds of things I am prepared to do to keep you properly, how should I put this…motivated. So what do you say," Jeremy repeated for the second time that day, "partners?"


	3. Chapter 3: Sara

Chapter 3: Sara

Sara opened the door to Lincoln's shop and embraced the feeling of the cool air on her face. Being eight and a half months pregnant in the middle of the brutal Panamanian was not what one would consider 'ideal' circumstances. But no matter how much she may complain about her pregnancy, whether it be the too hot environment made hotter with the extra twenty pounds she had put on thanks to her little bundle of joy due any minute now, or perhaps the swollen ankles and loss of ability to see any part of her lower body, Sara wouldn't trade this baby for the world: her little miracle, the last piece of Michael she had left. Some days she missed him so much she couldn't breathe. But she knew that no matter how much she missed him, or how bad her circumstances may seem, she knew if Michael were here, he would want her to take care of herself and their baby; their miracle.

Finally Sara closed the door to the shop behind her. As the door closed, the bell hanging above the door rang, notifying Lincoln that a new customer had entered the shop. "Good morning and welcome to Mike's Scuba Shop. How can I–" finally Lincoln looked up from his desk and saw his very pregnant sister in law standing in front of him. "Oh it's just you," he deadpanned.

"Gee thanks Linc it's good to see you too," Sara dryly replied even thought she inwardly smiled, as she always does when she hears Lincoln proudly welcoming guests to Mike's. Even though Michael didn't make it to Panama, Lincoln started up the scuba shop like they had always planned to. LJ helps out around the shop when he can, but is often busy with his college courses. Lincoln felt it was only right to name the shop after Michael. He had always said, "If he can't physically be here, at least his name lives on forever."

"You know I'm kidding sis," Lincoln started as he walked over to wear Sara was standing and greeted her with a hug and kiss on the cheek. "How are you feeling? How's Squirt treatin' ya?" Since Sara had decided to opt out on learning the baby's gender, claiming she wanted it to be a surprise although Lincoln thought it was solely to drive him crazy, the gang had taken to calling the baby Squirt or sometimes even Junior.

"We're doing pretty well. I'm more than ready for Squirt to make his entrance into the world though. Let's just say being eight and a half months pregnant in 100+ degree weather is not the most enjoyable thing in the world. Thanks for asking, Uncle Linc," Sara answered. Lincoln had truly stepped up as the baby's uncle. He went to every doctor's appointment, answered every late night phone call to pick up ice cream or pizza or whatever Sara desired. He insisted he owed it to his brother. To be honest, Lincoln always felt slightly guilty for his brother's death. After all, if he never would have gone down the wrong path and gotten entangled with the Company and thus sent to prison, Michael never would have even been a part of any of this mess. Yes, Lincoln definitely felt he owed everything to his brother.

"Good. Why aren't you at work?" he asked.

"Well," Sara began, "I just saw my last patient. I am officially on maternity leave since little Squirt could be making his debut at any moment now," Sara finished with a smile.

When they had first arrived in Panama, Sara couldn't eat or sleep, or even function without Michael. She would lie in bed all day, only eating when Lincoln or Sofia came by and practically force fed her. She knew that it wasn't good for her baby, but she simply could not help it. The pain of losing her one true love had been far too much for her to handle. However, after Lincoln dragged her to one of her routine sonograms, and she heard her baby's heartbeat for the first time, she knew it was time she start taking better care of herself. So, she went out and found a job at a local hospital. She of course had to start her residency over, and she chose pediatrics as her new specialty. Sara has loved every minute of her "new" job, and is extremely grateful that she is able to continue practicing medicine after everything that has happened.

Sara smiled and rubbed her swollen belly as she felt her baby moving around, interrupting her from her thoughts.

"Are you coming by later for dinner? LJ's coming back from Chicago today. Plus, Sofia is cooking, and I know how much you love it when she cooks." Lincoln smiled as he thought of his son. He was so proud of LJ for going to college at the University of Illinois at Chicago. After almost an entire semester of being at school, LJ was finally coming home after finishing out his freshman year and his spring finals.

Sara knew how excited Lincoln was to finally see his son again, but knew Lincoln would play it cool, claiming his son coming home after months in another country wasn't that big of a deal. She decided to gracefully decline the invitation, "Sorry Linc. I already made plans with my DVR and a box of pizza tonight. Thanks for the offer though. Enjoy the time with your son and girlfriend," she smirked.

As Sara thought of LJ in Chicago, she longed to return to Illinois and the United States in general really. As much as she loved her life in Panama, she missed her home. However she knew returning to the US would also mean her arrest, and as much as she longed to get back to America, she would not have Michael's death be in vain. Michael's tombstone was also here in Panama. Even though they hadn't been able to recover his body, she couldn't leave her last connection to Michael behind. She planned on taking little Squirt to visit him often, and tell him stories of his daddy that gave everything to ensure his safety.

"Okay," Lincoln's voice interrupted her from her thoughts, "but if you change your mind, you know you're always welcome. We gave you a key for a reason," he said as he winked at her. When they first arrived in Panama and Sara still wasn't sleeping through the nights as she would wake up crying out for Michael, Lincoln and Sofia decided to give Sara a key to their house. "Just in case," they had said, but Sara was extremely grateful, as Lincoln had been there for her whenever she needed him. Michael would be proud.

"Thanks Linc. For everything," she said. "I should get going, and you should too. If Sofia has to slave away over a meal for YOU, you should at least be there to keep her company."

"You're right, you're right," Lincoln laughed. "Be safe getting home. And take care of my nephew!" he shouted over his shoulder.

"Or niece!" she yelled back. "Bye Linc."

**Ah so Sara, Linc, and the rest of the gang finally make an appearance. The rest of the story will pretty much go back in forth between life in Panama and life at the Company Headquarters in Florida. A little bit of a longer chapter to reward any readers that are still out there. Hope you're liking the story so far. Reviews are always welcome! Let me know what you guys are thinking :)**


	4. Chapter 4: Time to Think

**Hey guys! So I know there was some confusion in the last chapter. I said Sara couldn't leave Panama even if her name was cleared because Michael was buried there, but I meant that his tombstone was there. Since Sara had to leave Michael behind in order to get out of the prison, it would have been impossible for her to retrieve his body and give him a proper burial. I've made some changes to the previous chapter to clear this up. Sorry about that!**

Chapter 4: Time to Think

"So what do you say," Jeremy repeated for the second time that day, "partners?" Michael's response included a whole lot of silence. He sat there and stared blankly at Jeremy. How in the world was he supposed to work for the Company; the very same people who destroyed his and his entire family's life? But if he didn't do as they asked, he knew the consequences would be unbearable. He knew there was no choice to be made, but Jeremy didn't know that. _I just need to stall him until I can figure out how to get myself out of this. That way, everybody wins, _Michael thought.

"Listen Jeremy," Michael began, "this is a big decision. You can't honestly expect to decide something this big in only a matter of minutes, can you? I need some time to think, and being the understanding man that I know you are, I assume you will happily give me said time," Michael smartly finished. "After considering my options _thoroughly_ I will get back to you with my answer. I hope this is okay with you."

Jeremy stared blankly at Michael. He said nothing for what felt like an eternity. Michael became a little bit nervous, afraid that his demands had been too far-fetched and Jeremy was about to make a call to certain guards in Panama that would shatter Michael's whole world. Michael imagined the worst possible fates for his loved ones, and when he couldn't bear to think of the possible tragic outcomes, he knew he needed to take back his previous statements and lessen his demands.

Just as Michael was about to make the deal, Jeremy finally spoke. "I understand your need for time with these kinds of serious, life altering decisions. However, know that if you refuse, we _will_ let you go, but only to watch us kill each one of your family members one by one, before finally killing you. However I do understand your need for time, and will therefore give it to you. Yes Michael, take all the time that you need," Jeremy finished with a knowing smirk. It was almost as if he knew Michael would accept the deal considering the new circumstances.

There was so much at stake surrounding one decision. Michael knew that the choice was already made for him, but he couldn't accept it. He would rather die than work for the Company, but he knew that if he tried anything, his family would be as good as dead. He couldn't risk that. No, he knew his answer. As unwilling as he was to accepting his new fate, he knew that he had to for the sake of his family. He hoped that one day, he could see his family again, or at least know and take joy in the fact that they had finally found peace and happiness. And although he missed Sara terribly, he wasn't worried about her fate. He knew Lincoln was taking great care of her and their child. _My gosh_, he thought. His child will be born any day, and he had no way of knowing when or if Sara and his child were healthy. This was the worst thought of all. He would never know his child.

As Michael thought of all the possible outcomes of his current situation, he knew that there had to be a way out of this mess. He grew more and more exhausted. It had been an eventful day, and he had been awake for just a few hours. Even though he had just woken up from sleeping for seven months, he felt like he hadn't slept in years. He returned to his cot, and decided to get some rest. He would need a clear head if he wanted to figure out a way to get himself out of this. With thoughts of Sara, his unborn child, Lincoln, LJ, and even Sofia on his mind, Michael finally drifted off to an anything but peaceful sleep.

**Sorry it's such a short chapter, but it's meant to be a filler more than anything else. Hope I still have a few readers out there. Let me know! :)**


	5. Chapter 5: It's Time

Chapter 5: It's Time

"Who's there?" Sara called out. She was afraid and cold. She saw a man in the shadows of the empty room. _How did I get here?_ Sara thought. Finally, the man emerged from the darkness, and Sara could not believe her eyes.

"Michael? Is that really you? I can't believe it! How is this happening? What are you doing here Michael?" Sara asked.

"I came back for you, Sara. I could never leave you and our baby. I love you both too much. We're going to live happily ever after," Michael told her. "But I can only stay if you help me."

"Anything," she said. "I'll do anything just please don't leave me again. Please," she pleaded feeling the tears well up in her eyes.

"I can't stay now. Help me Sara. Take care of yourself and our baby, okay? That's how you can help me, okay? I'll truly be at peace if you can do that for me. I love you so much Sara," Michael finished before he began to retreat from Sara's shaking form.

"Michael?" she called after him. "Michael! No! Michael, please don't leave me! I need you! I can't do this without you, please! Michael!" Sara cried out as she fell to her knees, her sobs and desperate pleas taking over her body. She couldn't believe this was happening.

Sara awoke with a start, sweating, panting, and calling out for Michael. Ah yes, the nightmares had returned. She rolled over and groaned as she looked at her alarm clock and saw that it read 1:17 AM. Her nightmares had mostly faded, but some days, specifically the days where Michael was on the forefront of her mind; they would return and bring nothing but heartache. This one was different though. It was so vivid. It was like he was truly there with her, calling out to her. In a daze, she tried to shake the feeling of him, but she couldn't help but feel that he was with her in that very moment. She could almost feel his arms around her.

As with all of her other nightmares, Sara knew there was no chance she was getting any sleep anymore. She felt she needed to be close to Michael. She hastily got dressed, got in her car, and drove the all too familiar drive to the place she felt closest to Michael; the place she went when the grief or her nightmares became too much for her.

* * *

Sara pulled over on the side of the road, and got out of her car. She knew the grounds of this cemetery too well. She then realized that it was 1:30 in the morning, and to any passerby, she would look like an absolute lunatic. After all, what normal person would walk around a cemetery while it was still dark out? She walked the same path she had all those other times, until she found Michael's tombstone. She sat down in front of it, her hands on her rounded stomach, and smiled at the inscription on the tomb.

"Be the change you want to see in the world," she read aloud. "Do you remember that ice breaker?" she laughed. "I knew I was in trouble the moment you walked into my office, with those brooding blue eyes and that boyish grin. God, that seems like a lifetime ago. I know if you were still here you would without a doubt be lecturing me about being almost nine months pregnant and wondering around a cemetery at 1:30 in the morning, so I'll go ahead and apologize for that offence," Sara said with a smile. "No, I'm here because the nightmares are back. Or at least they are for tonight. But there was something different about this one. It was so real, at least it felt real. But maybe it only felt real because I wanted it so badly to be. I wish you could come back to me. But I know that's not possible. I guess I'm just here because I needed to feel close to you."

Sara turned around and rested her back on the grave and sighed. She often found herself in this position. After what seemed like an eternity, Sara stood, knowing she needed to get home because she had to be at work in just a few short hours. She also had developed terrible indigestion over the time that she had sat with Michael, and really just wanted to lay down for a while before she had to go to the hospital for work. She turned and faced Michael one last time. She kissed her hand and pressed it against the stone, before turning her back, taking a deep breath, and walking away.

As she took her first step, she felt something warm run down her leg. She looked down, and noticed she was standing in a puddle. Her water had broken. Sara stood in shock for a few seconds, before frantically searching through her purse for her phone. Once she found it, she dialed the familiar number of her brother in law. Turns out her indigestion had actually been contractions. As she waited for Lincoln to pick up, Sara once again slid to the ground, so her back was against the tombstone of her husband.

* * *

Lincoln groaned and rolled over as he heard the shrill ring of his cell phone. He would have ignored it, except it was a call from Sara. He knew if his brother was watching over him, and saw that he had ignored a phone call from his very pregnant wife regardless of the fact that it was, Lincoln looked at his alarm clock, three in the freaking morning, he would haunt his ass for the rest of eternity.

"This better be good Sara. It's three AM and I–," Lincoln began before a frantic Sara interrupted him.

"Linc! I need you to come get me now! My water broke and my contractions are getting closer together. Please hurry!" Sara's frantic voice cut him off before he could finish.

"What?!" Lincoln shouted back. "I'm on my way. Where are you? Are you at home?"

"No..." Sara sheepishly started. "I'm at the cemetery."

"I'm not even gonna ask," Lincoln answered. "I'll see you in ten. And for god sakes Sara, keep your knees together. You are not about to give birth in a cemetery!" he said with a laugh before hanging up the phone.

Lincoln hastily wrote Sofia a note explaining where he was and for her to call him when she woke up. He kissed her forehead, before sprinting to his car, keys and overnight bag in hand. _I'm gonna be an uncle_, he smiled. _Shit! Sara's gonna be a mom!_, he thought as he speeded out of his driveway and headed toward the cemetery.

**So there's chapter five! Hope you enjoyed it, and hope that I still have a few readers left :)**


	6. Chapter 6: Michael Scofield

Chapter 6: Michael Scofield

Lincoln pulled up to the cemetery and put his car in park. He had no idea it was possible to get across town in so little time. He ran from his car to his brother's grave, and saw his sister-in-law, obviously in pain, leaning against Michael's tombstone.

"Oh hey Linc," Sara greeted. "Nice of you to join the party," she panted out.

"God, Sara! Why would you be in a cemetery at," he paused to look down at his watch, "3:30 in the morning?"

"I wanted to be close to Michael. And it seems like Squirt here wanted to join the party. He wanted to be with his daddy just as much as I did." Sara grunted as another contraction hit her, and Lincoln was at her side in an instant.

"Okay," Lincoln started, "we need to get you to a hospital. Like now."

"Well thank you Dr. Lincoln for your expert opinion," Sara retorted sarcastically as the contraction ended.

Lincoln grabbed Sara's hand and helped her to his car.

* * *

He got to the hospital in record time and was rushed inside with Sara trailing behind him.

"Hi," he greeted the desk nurse at the hospital.

The sound of her newborn's cries filled the air as Sara collapsed gasping for breath back onto her pillow.

"It's a boy!" Sara heard her OB cry out.

Suddenly, Sara's whole world faded out around her. Everything was a blur. All she could seem to focus on was the little bundle of blue that Lincoln was holding as he made his way over to Sara.

"You did it Sara. He's here. He's here, and he's beautiful," Lincoln said with nothing but admiration in his voice as he laid her newborn son on her chest. She stroked his chubby cheek and smiled at her miracle baby, her last piece of Michael.

"Hi baby," she greeted. "I'm your mom. And I'm gonna love you forever," Sara half chuckled, half sobbed out. She couldn't believe he was here. He was even more perfect than she imagined.

* * *

Sara cradled her newborn son closely to her chest. Lincoln had just left to go call Sofia and LJ to tell them the happy news. Her beautiful son had been born 20 minutes ago, and this was the first time she was truly alone with him, without any interruptions from nurses, doctors, and even her family. Her baby boy was absolutely perfect. At 7lbs 3oz, and 22 inches long, he had already completely stolen her heart. He had yet to open his eyes, but she knew that when he did, they would be blue. Now, all newborns had blue eyes, but she knew his blue eyes would stay.

At just 20 minutes old, her little baby had already proven to be the carbon copy of his dad. Quiet, but always looked thoughtful; or at least as thoughtful as a 20 minute old baby could look. She could already tell that her son was going to be quite the heartbreaker, just like his father.

Sara's heart painfully squeezed for a moment as she once again thought of Michael. She would have given anything for father and son to have a chance to meet, but she knew there was no such option. She lovingly gazed down at her son, and that's when she knew. She knew what his name had to be.

As Lincoln reentered the room he said, "Well if it isn't my two favorite Scofields." He made his way over to Sara's bed, and sat in the chair next to it. "Hey little guy, remember me?" he whispered as a greeting. Sara smiled at the interaction. She knew her son and Uncle Linc were going to have a very special bond. Through eight long hours of labor, Lincoln hadn't left her side, besides to get ice chips when requested. He truly had been her rock.

"Any luck with the name?" Lincoln's voice interrupted her from her thoughts.

"Actually, yes. I've been doing some thinking and I've decided. So, Uncle Linc, I would like you to meet your nephew _and _godson, Michael James Scofield II, Mikey for short" Sara finished with a smile and a wink.

"Godson?" Lincoln questioned, dumbfounded.

"I wouldn't have it any other way, and neither would Michael. You've truly been my rock, and I don't know if I could've made it this far without you."

At the mention of his late brother, tears formed in his eyes. He was so proud of how far Sara had come. "Of course I'll be little Mike's godfather. I couldn't imagine a greater honor," he finished before leaning down to envelop Sara in a warm hug.

"Perfect," Sara smiled.

"Can I?" Lincoln asked, implying he would like to hold his baby nephew.

"Of course. Well then I guess everything's official now. Of course I'll have to ask Sofia to be godmother when she gets here, but other than that everything's squared away I guess," she finished. Her mind began to wander. She wondered what Michael would say if he were here. God, she missed him so much.

"He would be proud of you," Lincoln's voice interrupted her from her thoughts. "He's got the biggest smile on his face right now, I just know it." Lincoln smiled a bittersweet smile as he thought of the son his brother would never get to meet. "I know he wishes he could be here to do this," Lincoln continued, "but since he isn't, I'll do it for him." Lincoln smiled down at the sleeping baby in his arms, "Welcome to the world, Michael James Scofield II. I'm not your daddy, but I know that even though he can't be here, he loves you with all of his heart." Lincoln finished.

Sara smiled at the pair and knew in her heart that her son would never go a day without knowing how much he was loved by his father, thanks to his Uncle Linc. With this thought in her head, she knew she could do this. She knew she wasn't alone, and she knew no matter what, she was going to love her son until the end of time.

"Well," Lincoln started, "I'm gonna go and let you get some rest. Looks like this little guy has just drifted off as well, so I'll put him down and let you do the same," he said as he made his way over to Mikey's bassinet. He kissed his head, before gently laying him down next to Sara's bed.

He then made his way over to Sara's bed and kissed her on the forehead. "Get some rest, you deserve it. I'll be back in the morning with the rest of the gang to meet little man."

"Okay, night. Oh, and Linc?" Sara called after him.

"Yeah?"

"Thanks. For everything," she said with a smile.

Lincoln just smiled and winked at her, before turning around and leaving the hospital room, closing the door behind him. Sara finally relaxed and closed her eyes with Michael and little Mike fresh on her mind.

**A/N So there you have it, chapter 6. Back-to-back Panama chapters, but not to worry we'll be back to Jeremy Krantz and Michael next chapter. I didn't actually know Michael's middle name, only that it started with a "J", so I figured James was a good fit. Hope you are all still enjoying this story. Reviews make my heart happy!**


	7. Chapter 7: Motivation

Chapter 7: Motivation

"I got the picture," Jeremy heard from the other end of the call. "How would you like me to proceed?" the Company spy watching Sara as she sat with her three month old son in her arms in front of Michael's tombstone asked.

"Are you sure you can clearly tell who is in it?" Jeremy asked in return.

"Yes sir, I am positive," he answered.

"Perfect. Email me a copy of it ASAP."

It had been months since Michael had requested more time to think, and with each week that passed by, Jeremy Krantz became more and more impatient. Of course, he couldn't deny Michael the time he had requested, for Michael would in return refuse to ever work for the company if any harm came to his family. Yes, now that his _son_ was born, Jeremy had some new leverage.

"Good morning Mr. Scofield. Hope you slept nicely. Any progress with the decision making?" Jeremy asked as he had done every day for the past three months. Every morning, Jeremy would bring Michael his breakfast and repeat the same three lines; the exact same way, morning after morning. And in return every day, Michael would give the same curt response.

"No, sir. Still need more time to think, if that's all right with you," Michael answered shortly without looking up from the newspaper that came each morning on his breakfast tray.

Jeremy smirked. Each morning previous to this one, Jeremy had delivered the same response to this request, claiming that yes, more time would be given. But today, Jeremy had a different plan. He was no longer going to continue being the easy going 'boss' he had been in these past months, simply because he no longer need to. Yes, now he had leverage.

"Why yes, Michael. Of course you can have more time," Jeremy started, "but I don't think you will like the outcomes if you decide to take this 'extra time' to make your decision." It was then that Michael finally looked up from the paper with a scowl present on his face.

"What exactly do you mean Jeremy? I'm not sure I'm following," Michael responded.

"Well you see, Michael, I am a patient man, but even the most patient men have their breaking points. See, I believe that I have given you ample time to make this decision. So in order to speed up the process, I have found a new way to keep you, how should I put this, properly motivated." It was then that Jeremy reached into his coat pocket and pulled out the picture his guard had taken of Sara and Mikey in the cemetery. He put the picture face down in front of Michael.

"Go on," he said. "Turn it over and look at it. I guarantee you want to."

Michael, still scowling, picked up the picture. Upon turning it over, his features immediately softened. He traced over the faces of his wife and son with his fingers as he memorized the picture with love and adoration in his eyes. He had a son. And his son was perfect. And god, Sara was even more beautiful than he could've remembered. While they both looked happy, he could see the sadness in Sara's eyes. It was then that he realized where they were sitting. They were in front of his tombstone. Suddenly the happiness in love shown on Michael's face disappeared. It was then that Jeremy's voice interrupted his thoughts.

"Now isn't that just the perfect family picture. All that's missing is Daddy," he started as Michael glared at him. "In case you were wondering, his name is Michael James Scofield II, which is fitting because he looks like your double. Sara has taken to calling him Mikey, while his godfather leans toward Little Mike. Oh, his godfather is Lincoln, did I forget to mention that? Ah yes, young Michael has many nicknames. Your nephew, LJ is it? Well LJ has taken to calling him 'MJ'. Isn't that just adorable?" Jeremy finished with a gleam of mischief in his eyes.

"What are you trying to prove here?!" Michael demanded angrily.

"I'm trying to prove that my kindness should not be taken advantage of and should not be mistaken as weakness!" Jeremy retorted with just as much anger.

Michael couldn't speak. He couldn't breathe. He had a son, and yet if he didn't agree to do the one thing he had always sworn to never do, his son, his precious gift, could be ripped away from Sara. His glare finally softened.

"What do you want from me?" Michael asked defeated.

"I think we both know the answer to that question, Mr. Scofield. The true question is what are you willing to do to give me what I want? And what am I willing to do to make sure you do what I want?" Jeremy asked. He liked these circumstances much better. He finally felt in control. His father would be so proud, he knew it.

"So Mr. Scofield," Jeremy started once again, "what's it gonna be? Time's a-wasting," he finished with a smirk.

They sat in silence for several minutes. Michael knew what he had to do, but couldn't bring himself to say it. He knew what he must do, as much as it killed him. The Company was for everything he was against. Hell, he lost his family and nearly lost his life because of them! His brother was almost executed for a crime they had framed him for! For God's sake, they let him believe Sara was dead for weeks! He had lost everything because of the Company, and now? He was going to help them build themselves back up from the ground, after everything they went through to destroy them. He never thought the next words he said would truly come out of his mouth.

"Okay," Michael finally concluded. "I'll work for you."

"Ah, I'm glad you've finally seen the light. I cannot wait to get started. Your potential astonishes me," Jeremy finished with a smile.

"Not so fast. I have a few demands of my own," Michael began. "First, I want Sara and Lincoln's names cleared of all charges. I don't care how you do it, but get it done. I want them to be able to return to the US if they so desire. Next, I want your word that no harm will come to any member of my family. And finally, I want pictures every month of my wife and son to prove that they are alive and well," Michael finished. If he was never going to get a chance to meet his son, he wanted to at least get to see him grow up, even if only through pictures.

"Done, done, and done," Jeremy said with an eager smile. "I cannot wait to begin our work. Oh but in return, as I am about to become the head of an extremely powerful corporation, people cannot know my true name. I insist that you now refer to _me_ as the General," Jeremy ended before turning to leave the room. Before walking through the door, he turned to Michael one last time. "I'm glad you have made the right decision. Your work starts first thing tomorrow," he said before finally walking out the doors.

Michael picked up his glass of water and threw it against the wall as he screamed in frustration. He couldn't believe this was his life now.

**So there you have chapter 7! My update speed will be slowing down for a while, as I'm heading back to school. I'll update as frequently as possible, and write as often as I can! Hope there are still at least one or two people still reading. Feedback is always welcome and wanted. Read & review! :)**


	8. Chapter 8: Free

Chapter 8: Free

Sara groaned at the sound of her five month old son crying accompanied by the flashing lights on the baby monitor on her bedside table, signifying that her son was awake. She rolled out of bed and walked out of the room. She padded down the hallway until she reached Mikey's room and opened the door. Her son's wails became louder and louder. Man, she was impressed with the set of lungs on this kid. She walked over to Mikey's crib and picked him up.

"Hey, little guy," she greeted. "What's all the fuss about, huh?" she asked in a soothing tone. She walked over to the rocking chair in the corner of the room and sat down as Mikey's cries softened to whimpers before falling back asleep.

Sara rocked him in her arms and looked over at the clock in Mikey's room. It read 2:32 AM, which meant she still had a solid three and a half hours before she had to be awake to get ready for work. She was actually surprised Mikey had woken up in the middle of the night. She thought he had grown out of that, but she didn't mind. She loved her son with all of her heart, and would do anything for him. Even if that 'anything' included 2 AM mommy snuggles.

She laid Mikey back in his crib before walking back to her room to get some much needed rest before work.

* * *

At 6 AM, Sara's alarm went off, and she rolled over and shut off the annoying, repetitive buzzing noise filling her room. Every morning, her routine was the same, or at least every morning since she returned to work and Mikey began sleeping through the night for the most part. She climbed out of bed and hopped in the shower, getting ready for work as she had done every morning prior.

20 minutes later, Sara emerged from the shower clean, and changed for work, just in time to hear her son crying, signaling that he was awake, and ready to be entertained. Sara made her way to Mikey's room, and retrieved him from his crib, immediately soothing his cries. She brought him to the kitchen, set him down in his high chair, and brought him his jar of mushy pears for breakfast.

After she finished feeding a very squirmy baby, Sara wiped off the leftover pear from Mikey's chubby cheeks, and took him to his room to change him for his day. One of the many downfalls of living in Panama was that the hospital where Sara worked didn't have a daycare center where she could leave Mikey while she worked. Thankfully, Sofia was more than happy to watch him when she could, however there were days Sofia was busy, and Sara would have to find other arrangements for Mikey. It was times like these when Sara longed to return to America.

Sara's thoughts were interrupted by the ringing of both her cell phone and doorbell at the same time. She saw that it was Lincoln who was calling and picked it up right away.

"Hey Linc," Sara greeted.

"Hey. Sofia's sick today, so I closed the shop for today and can watch Mikey for you."

"Thanks Linc, I owe you."

The doorbell rang again, and Sara picked up Mikey and put him in his playpen before making her way to the front door.

"Is that a doorbell? Who's visiting you at 6:30 on a Tuesday morning?" Lincoln asked.

"I have no idea," Sara chuckled, "but I'm about to find out," Sara finished as she opened the door.

Sara dropped her phone to the ground when she saw who was on the other side of her door. She couldn't believe her own eyes. She immediately wanted to slam the door in her surprise visitor's face and take her son and hide. How had the US Ambassador found her? And more importantly, was he here to take her back to prison and away from her son?

She could faintly here Lincoln's voice frantically calling her name on the other line, but she couldn't be bothered to answer him right now. The Ambassador was talking to her about the new circumstances of her current situation, yet Sara couldn't seem to find words to form to respond to him. Eventually he picked up on the fact that she was not in the talking mood, thanked her for her time, apologized for the inconvenience, and then left her house. Sara was shell shocked. She walked back to her living room and sat on her couch trying to process everything that had just happened. She knew she was going to be late for work, but it didn't matter. She was too shocked to move.

* * *

"Sara? Sara!" Lincoln shouted to the phone line that just went dead. He was panicking. Lincoln quickly found his car keys, and made the familiar drive to Sara's house. He knew he was probably being paranoid, but he once promised to his brother that he would protect Sara until the day he died, and he was not about to go back on his promise now. Plus, better safe than sorry, right?

He used his key to open the door, because he figured if she was kidnapped or tied to a chair being held for ransom, there was no point in wasting time with formalities like doorbells and knocking. He was thankful to see his sister in law sitting on the couch, indicating that she had not been kidnapped, and was indeed, not being held for ransom. However upon getting a closer look at her, he grew worried. She was pale, no scratch that. She was white as a sheet.

"Sara?" he said quietly, afraid of startling her.

Sara noticeably flinched before relaxing when she realized it was just her brother in law.

"Oh hey Linc," she half-heartedly greeted. He could tell something was wrong, and he had a sneaking suspicion it had something to do with her unexpected visitor this morning.

"What happened? Who came by this morning?" Lincoln anxiously asked.

"It was the US Ambassador," Sara shakily responded.

"What? He's not taking you back to prison is he? Because I'll fight them, I swear I will fight them with everything I have. They will not take you away from Mikey. God they already took his father away, and now they want his mother too? Well over my dead body. I can't believe they're doing this to you, after everything you've been through, after everything we've been through! We can contact Kellerman. He's running for office or something, right? We'll fight this Sara, and we'll win. Don't worry. I'm not letting anything happen to you, or Mikey. Well? Sara?" Lincoln finally said, finishing his rant.

"They didn't come to take me back to prison," Sara began. "They came to tell me that my name, all of our names: yours, mine, Michael's, have been cleared of all charges."

"Wait so you're saying that…" Lincoln began with disbelief evident in his voice.

"That we can go back. We can return to America. We can go home. It's finally over," Sara finished with what felt like the first genuine smile she had smiled in ages.

**A/N So it looks like things are finally looking up for Linc and Sara. Sorry it's been so long since my last update, but school's got me slammed. I'll try to post at least once a week! Reviews really make me want to write more though ;). Let me know if you're out there are reading! XOXO**


	9. Chapter 9: A New Partner

Chapter 9: A New Partner

Michael woke to the sound of the loud P.A. system in his room that had conveniently, conveniently for the Company at least, become an alarm clock for the Company's use. They could use it to wake him up pretty much anytime they felt like it. It was the most unpleasant wakeup call he had ever had the displeasure of experiencing. But, he knew he had to wake up, as the 'new General' would be in any minute with Michael's agenda for the day. He was already dreading that.

It had been three months since he began working for the Company, and so far he had made good progress, but he was secretly holding back. He knew eventually the General would figure out that Michael was withholding all of his talent, but for now it was the only leverage he had. If he gave the General everything he wanted, there would no longer be any reason for him to keep Michael alive. So he was working a little bit slower than he should have been, but the General seemed pleased with the progress that had been made, and Michael planned to keep up this charade for as long as he could.

After Michael had been up for what felt like hours, but was really only about twenty minutes, the General entered the room. He looked pleased, as always. He was probably just excited that he was able to get his hands on the only mind that was even more brilliant that the Christina Scofield's.

"Good morning Michael. I do hope that the wakeup call wasn't too early, and that you have rested well," the General greeted.

"Slept just fine. What's the plan for today?" Michael asked curtly. He didn't feel the need to waste time on small talk with his captor. They weren't friends, and they were never going to be friends. Therefore, Michael did not feel the need to 'play nice'.

"Well since you are so eager, as always, to get started, I do have a little treat for you. You know, to say thank you for all of your hard work," Jeremy finished with a smirk.

Michael's mind began to wander to all of the terrible things that 'the General' could have planned for him. Was it going to be more pictures of his family? As much as he loved seeing his beautiful wife and son, he absolutely hated the fact that Company agents were so close by that they could their pictures while remaining undetected. It killed him inside to know that his family was completely unaware that they were actively being watched, and there was nothing he could do about it. He wished more than anything that he could somehow warn them of the danger that always seemed to find them someway, but he knew that couldn't happen. So for now, he would have to cooperate with the General until he could somehow figure a way out of this mess. He would do whatever it took to get back to his family, even if it meant feigning a little enthusiasm for his 'surprise'.

"Well I can't wait to see what you have in store for me today," Michael finished with a tight smile.

"Well when you put it that way," the General began as he made his way over to where Michael was standing, "I figure that building a multimillion dollar company from the ground up is not an easy task, and you can use all the help you can get. So I took the initiative in hiring one of your former cohorts to make your job a little bit less stressful."

Jeremy made his way over to the intercom on the wall. He pressed the button and said, "You can come in now," before turning back to Michael with a smile.

Michael eyed him suspiciously, before turning his attention back to the door to await the arrival of his newest 'surprise'.

"Hello Michael."

Michael couldn't believe his eyes. Alex Mahone was standing in front of his very eyes. He was shocked. For one because Alex was standing right in front of his face, but also because he couldn't believe that Alex could willingly work for the Company after everything they did to Pam and especially Cameron.

"Alex," Michael offered as a greeting. "What are you doing here?"

"Allow me to explain," the General interrupted before Alex could speak. "You see, I found your old friend here, unemployed and drinking away his sorrows alone in a bar one night. After helping you in your escape from Miami Dade, the FBI refused to rehire him, and well with his growing criminal record, not many people would. So I offered him a job, explaining to him the new situation, and I of course informed him of your involvement in the rebuilding of the Company. Once I laid it all out on the table for him, Alex happily accepted the job. See Michael? Not everyone is so intent on holding the grudges that you and your family seem to so desperately cling to."

"How could you do this Alex? You're practically throwing away the life that you fought, that we all fought for so desperately. How could you work for the same people who gave the order to kill your son?" Michael said in outrage. He was furious. He would do anything to get his old life back, while Alex was throwing his away, and for what? A little extra cash?

"Well Michael, if it weren't for you I wouldn't be in this situation. I felt indebted to you, and I risked it all in hopes that my FBI agent girlfriend would be able to convince the bureau to take me back. Well guess what? She couldn't. And I couldn't stay unemployed for much longer, so you know what I did what I had to do. It is your fault that I'm in this situation, and I am going to make you pay," Alex finished out as his rant came to an end.

"Well it's clear that you two have a lot of catching up to do now, so I'll leave you to it. And don't worry about getting any work done today. Your new partnership can begin tomorrow," the General finished before leaving the room.

"What the hell man? After everything I've done for you? After everything we've survived together? You're just gonna screw me over like that? How could you? I thought our friendship actually meant something. No one forced you to help us break Sara out of prison, okay? I thought you were doing it to save her life because you cared, but if it messed your life up this much, you shouldn't have even agreed to help us. We could've figured it out without you, and you know what? I would've preferred figuring it out without you than to have you hate me so much that you would actually willingly work for the Company," Michael finished with a frustrated sigh.

"Would you just shut up for two seconds?" Alex questioned. "That story was our cover. I'm here to get you out of here."

**A/N: Aha the boys are back together! I hope you enjoyed this chapter, and I'll update as soon as I can. As always I love reviews, so feel free to tell me what you're thinking about this story! Thanks guys! XOXO**


	10. Chapter 10: USA

**A/N So I'm officially the worst. So sorry it's been so long since I've last updated. I've been super busy, but am going on a road trip today and hope to get a lot of writing done! Anyway to make up for my absence, here's a bittersweet, somewhat fluffy chapter. Enjoy!**

**Ch. 10: USA**

Sara rocked her nine month old son in her arms in an effort to soothe him. She didn't know why he was acting like this. Overall, Mikey had proven to be his father's son in that he was always pretty calm, cool, and collected. He rarely had temper tantrums, but when he did, look out world. His incessant crying often made Sara nervous that he would stop breathing, or something, because of his loud shrieks and beat red face. She could usually calm him down pretty easily, but for some reason today was just one of those days where Mikey could not be soothed.

Sighing, Sara made her way over to the cabinet where she kept everything she had left of Michael: a couple of his shirts, the origami flower, and the DVD he made for her and Linc to watch. She reached for the DVD, and walked over to the DVD player. She put in the disk, turned on the TV, and was once again amazed by her husband's ability to bring a sense of calmness to any given situation, even from the grave. Almost immediately upon seeing his father's face and hearing his soft voice, Mikey's cries died out as he watched his father on the screen.

It was then that she heard it. It was…soft, almost like a question. But upon hearing it, Sara's face broke into the biggest smile she thought she would ever smile. Her son, her precious baby had just said his first words. Now granted it was hardly a word, and could possibly be overlooked by some as incessant infant babble, Sara knew there was no way in the world that it could be nonsensical chatter.

"Da da," her son called out as he waved his arms and pointed at the screen at his father. There was no doubt in her mind that Mikey had no idea what his father was saying, but it didn't matter. Her son knew who his father was, and that fact made her heart soar.

"Yeah buddy," Sara beamed. "That's your Daddy."

When the video ended, Mikey was calm, and on the verge of sleep, probably exhausted from his incessant screaming and crying from his temper tantrum. She took him to his room, kissed him on his forehead, and laid him down in his crib. She smiled as she saw the smile form on his face as he dozed off, the same way it always did, and the same way Michael's used to.

* * *

Sara walked back to the living room, and collapsed on the couch. She was wrecked. Watching that video, although necessary to ease her son's mental state, always took a lot out of her. She missed him so much. It was days like these where she longed to return to the cemetery where Michael was buried, just to feel like she still had some sort of connection to him; to feel closer to the one who stole her heart. But she knew she couldn't do that.

A few months ago, Sara, Lincoln, Mikey, and Sofia returned to the United States. After discovering all of their names had been cleared of all charges, Lincoln insisted they return to the place they knew as home. Sara was reluctant to leave, because she didn't want to leave behind her husband's grave, or Linc's scuba shop that he had always dreamed of owning. So they compromised. Every year on the anniversary of Michael's death, they decided that they would return to Panama for a few days to visit his tombstone. As for the scuba shop, it was in an ideal location, and was not hard to sell.

They moved to Florida two weeks after Sara found out her name had been cleared. While Linc knew Sara truly wanted to return to Chicago, Sara insisted that Lincoln could not give up on his dreams. They moved to Miami where Linc opened up a new and improved "Mike's Scuba Shop" on the Florida coast. He was content with how well his business had been doing, and happy to be back in the states.

Sara had received many job offers from several Miami hospitals, and decided to choose Miami Presbyterian, because it had the best pediatrics program, and offered a day care where she could drop off Mikey during the day. Of course she loved having Sofia watch him, but she loved being close to Mikey all day more.

Sara's thoughts were interrupted by the sound of keys jingling in the locks. She tensed only for a second before realizing that it was just her brother in law coming to check in on her.

"Hey sis," Lincoln greeted. "Where's my favorite nephew?"

"Sleeping," she responded as she met Lincoln for a hug.

"So how has your day off been? Have I missed anything exciting?" Lincoln inquired.

"Well actually, now that you mention it, Mikey may have a little surprise for you when he wakes up, which should be any minute now," Sara finished proudly.

As if on cue, sounds of Mikey's babbles filled the room and Lincoln immediately seized the opportunity to greet his nephew. Sara smiled at her brother in law's eagerness to see his nephew. They truly had a special bond.

As Lincoln entered the room, Sara caught the end of his conversation with Mikey, which mainly consisted of Mikey babbling excitedly and Lincoln smiling and nodding.

"Hi baby boy," Sara greeted in response to her son's outstretched arms toward her upon noticing her sitting in the living room. She plucked her son from Linc's arms and cuddled him close to her chest, kissing him on the back of his head.

"Did you have a good nap?" she asked not really expecting an answer

Lincoln smiled at his sister in law and nephew. He would give anything to have his brother here to witness this moment. He was so proud of the mother Sara had become, and how far she had come in coping with her grief. He knew the pain had to be unimaginable, but he also knew that having Mikey with her, her little piece of Michael, helped ease the ache in her heart. At least, he knew it did for him.

"Hey bud," Sara started, "are you ready to show Uncle Linc what you learned today?"

Mikey looked on at his mother curiously. Sara grabbed the TV remote, turned on the TV, and pressed play on the DVD player. Michael's face filled the screen.

Mikey squealed excitedly upon seeing his father's face. He waved his arms enthusiastically before pointing at the screen, looking at his Uncle Linc, and saying the very name that filled Sara's heart with so much joy.

"Dada."

**A/N So there you have it. Thank you guys for continuing to read! Next chapter we'll be back to Michael, Mahone, and the General. Reviews are always welcome! XOXO**


	11. Chapter 11: The Plan

Ch. 11: The Plan

_"Would you just shut up for two seconds?" Alex questioned. "That story was our cover. I'm here to get you out of here."_

Michael blankly stared at Mahone. He didn't know what to say. He didn't even know what to think. He had dreamed for months now of escaping this place and returning to his family, but he had no way of doing so. Now, someone was here, offering to help him find his way out and suddenly Michael wasn't so sure of his decision anymore. He was terrified. For the first time in awhile, Michael was truly terrified.

"Why are you doing this? Why are you helping me? You said so yourself that I ruined your life and your chances with the bureau, so why are you helping me?" Michael finally voiced after what seemed like hours of silence.

"Listen Michael, I only said those things so the 'General' would believe me. In order for this to work, he has to believe that I truly despise you. But in reality, I'm working with the bureau. Yes, they were angry when I helped you and Sara escape, but Felicia was able to plead my case to a higher power claiming that I helped you out of loyalty, an important trait for an FBI agent to have. When the General approached me in that bar, and told me he was planning on rebuilding the Company with your help, I knew I had to get you out of here. I knew there was no way in hell you'd be willingly working with these people, and sure enough here you are being held against your will. I'm helping you Michael because we're friends. You once risked everything for me and my family, so I will do everything in my power to get you out of here and back home to Sara and little Mike."

At the mention of his son's name, Michael's head snapped up.

"You've met him?"

"Yes. And Michael, he's beautiful. He's everything good about you and Sara. And god, he's so smart. He's only nine months old, but he is brilliant. He gets that from you. You deserve to know your son. I will do absolutely everything in my power to bring you back to him." Mahone finished.

Michael sat and thought about his choices. He knew there was no choice to be made, but he also knew that he would be putting his family's life in danger once again by escaping. He knew he would have to end the Company once and for all if he ever even hoped of living a normal life again.

"Okay," Michael concluded. "What's the plan?"

Mahone broke into a smile and said, "I thought you'd never ask. The trouble is that we have to escape in the middle of the day, as that's the only time we'll be allowed to be together. Now, the General does trust me more than you, but is still giving me limited privileges. I am not allowed out of my room after 11 PM, and I don't have access to any of the hidden labs or rooms without the approval of someone with greater authority. So that's what makes this a little tricky. Any ideas?"

"You wouldn't happen to have the blueprints for this place lying around somewhere would you?" Michael joked.

Mahone laughed in response. "No Scofield. I can't say that I do."

"I figured as much. I've been here for a year now, and I've picked up on a few things: a few kinks in the system in you will. For instance, all locked doors to the secret labs and exits require a keycard and fingerprint access. The keycard will be easy. All we'll have to do is demobilize a guard and we have our key card. The trick will be getting the fingerprint." Michael finished.

"And how do you suppose we do that?" Mahone questioned.

"Can you get ahold of some bubble gum and some tape?"

"Probably. But I don't see how—"

"You underestimate my planning, Mahone. It's rather insulting. We, and by we I mean you because I'm not allowed out of my room without an army of guards, will have to wait and watch for a guard to access a room. After said guard accesses said room you will put the tape on the access point and use it to lift the guard's print. Then you will immediately come back here where I will be waiting so we can recreate the print for use with salt and bubble gum." Michael finished proudly.

"Not sure I'm following, but alright go on." Mahone sighed.

"Once we have a guard's prints, and please pick a deceivable or wimpy guard, we will dismantle him the day of our escape, steal his card, and use his thumbprint to have access to all of the secret labs."

"Okay, but you've still failed to answer probably the most important question there is. How do you expect us to get past the two guards outside your room?"

"Always underestimating me, aren't you Mahone? We aren't going out through those doors. We're getting out through that." Michael finished as he pointed to the air vent located right above where he and Mahone were standing.

"We can never just have a normal, walking escape plan, can we?" Mahone asked incredulously.

Michael laughed in response and Mahone soon joined in. It was amazing how far they had come in just over a year. They had gone from chasing each other cross country, to working together to escape from the most powerful organization in the world. Oh how times had changed.

When their laughter died down Michael sobered and said, "I don't think I'll ever be able to repay you for what you're doing for me. You're giving me a chance to know my son, to love Sara, to have a family. There is no amount of gratitude to encompass how grateful I am. I have no idea how I'm going to make this one up to you."

Mahone walked over to where Michael was standing and clasped his hand to Michael's shoulder. "You already have. You have done so much for my family and me: helping me escape from Sona, finding Wyatt so I could give that son of a bitch what he deserved, helping me keep Pam alive with that crazy ass plan to save Linc AND Sara. So consider us even," Mahone finished as he held out a hand to Michael.

Michael chuckled and met Mahone's handshake, "Alright. Partners then. Oh did I forget to mention my favorite part of this little plan?"

"Oh yeah? What's that?"

"Let's just say we're going to get a front row seat while we watch the Company burn."

**So there you have it- a little inside scoop to Michael and Alex's plan. Sorry if the update time was too long, but things have been pretty hectic lately. Who knows, maybe if the reviews start coming in I'll even have a second chapter out by the end of the week! We shall see. Thanks for reading. R&R. XOXO**


	12. Chapter 12: Reunited

Ch. 12: Reunited

Sara was awoken to the sounds of her son's happy babbling coming over the baby monitor. She smiled as she heard him have a conversation with himself. It was times like this that she loved the most. But it was also times like this that she had Michael here to share them with. She imagined a life where they could lay in bed together and admire their son's creative mind. He was such a happy baby. All he needed in his life was his father. And all Sara needed in her life was her husband.

She rolled out of bed and made her way down the hall to Mikey's room. She opened the door and her son's conversation with himself ceased as his head snapped up in her direction.

"Mama!" He shouted playfully and threw his arms in the air. For ten months old her baby was a genius.

"Good morning handsome. Did you sleep well?" Sara asked after picking up Mikey from his crib, placing a kiss on the side of his head, and settling him on her hip.

Mikey started babbling and going on and on about things that probably made sense to him in his ten month old brain, but to the average human just sounded like pure gibberish. Sara nodded along and pretended to understand even remotely what he was saying, but felt only pure joy when he would notice she wasn't listening and grabbed her face between his small hands, saying, "Mama," to re-command her attention.

Sara set him down in his high chair and began to prepare his breakfast as she did every morning. After successfully getting about half of the pureed bananas in his mouth and the rest on the floor, Sara picked Mikey up and took him to his room to clean him up for daycare.

20 minutes later, she and Mikey were both dressed and ready for their days. Sara buckled him into his car seat and began her daily drive to the hospital. She had only been driving for a few minutes when her phone began to ring. She saw it was Lincoln and picked up.

"Hey Linc, what's up?" Sara greeted.

"Morning sis. Can we meet for lunch today? Bring Mikey." Lincoln cryptically stated.

"Umm sure, but can I ask why?" Sara responded curiously.

"Let's just say I have an…old friend who wants to see the both of you. Anyway I gotta go, but I'll meet you in the hospital cafeteria around 12:30. Alright see you then." Lincoln ended before hanging up.

Sara was dumbfounded. She hadn't heard this much excitement in Lincoln's voice in a long time. She was anxious for lunch to see what had gotten her brother in law so excited.

She pulled into her parking spot and walked around to car to unstrap Mikey from his car seat. She made her way toward the daycare center.

"Dr. Scofield, hi!" greeted Katie, one of the ladies who looked after the kids during the day.

"Katie, how many times do I have to tell you to call me Sara?" Sara scolded.

"Right. Sorry. How's our little man doing today?" Katie asked.

"Great! He slept great and is a great mood."

"Well when is he not?" Katie asked. "He'll be in great hands here."

"He always is," Sara smiled. "I'll be back around 12:15 to take him out for my lunch break, and then I'll bring him back. Thanks Katie," she said as she handed Mikey to her.

"Bye baby be good," Sara finished as she kissed Mikey on the cheek and left.

Sara started her day as she always did. She made her rounds, checked in on some of her recovering patients. She loved her job as a pediatric surgeon and wouldn't trade it for the world—except for maybe her husband.

After stopping in to check on her recovering patients, Sara made her way to the nurses' station to see if any cases needed her consult. She asked Sydney, her favorite floor nurse, if she had any consults and right when she was about to answer, her 'favorite' person came up to her and threw his arm around her.

"Hey gorgeous. How's the prettiest doctor at Miami Pres?" he tackily greeted.

"Well hello to you to Josh." She groaned and she slid out from under his loose grasp over her shoulders.

Josh was a plastic surgeon at Miami Presbyterian, and possibly the most difficult part of Sara's job. The trouble with Josh, is that unlike the other men who had shamelessly hit on Sara since she began working in Miami, he simply could not take a hint and realize that she was just not interested. Sure he was good looking and all that jazz, but that's where his good traits ended. He had the personality of stick and all he liked to talk about was himself and how great he was. Sara knew all he wanted to do was get in her pants, and there was no way in hell she was about to let that happen. Besides, she was nowhere near being over Michael.

"So how about that dinner date?" Josh asked for what felt like the umpteenth time.

"Maybe some other time," Sara answered without looking up from the charts she suddenly found herself interested in.

"Okay, well you're missing out on a great catch. I hope you know that," Josh cockily smirked and slapped her butt before finally walking away.

Sara rolled her eyes and wondered if he would ever move onto a new girl that actually showed even the slightest amount of interest. She handed her charts back to Sydney and headed to the daycare center to pick up Mikey for their lunch date.

Sara walked through the doors of the hospital cafeteria, Mikey in tow, and saw Lincoln wearing the biggest grin on his face.

"What's got you smiling like that? Is it Christmas morning or something?" Sara joked.

"No. I'm just very excited because we have a very special visitor. Come on out now dude."

Sara's jaw dropped as she saw none other than Fernando Sucre standing before her very eyes. She threw her arms around him as best as she could while holding her son.

"Fernando! What are you doing here?" Sara asked dumbfounded.

"I was just passing through town and realized I haven't stopped by to see my 'nephew' yet. Is this him?" Sucre asked motioning toward the child in Sara's arms.

"It is. Mikey, I'd like you to meet your Uncle Sucre. Fernando, I'd like you to meet your nephew, Michael James Scofield II, Mikey for short. Though LJ has taken to calling him MJ and Linc here has taken to calling him little Mike." Sara chuckled.

Sara, Sucre, and Lincoln spent the remainder of Sara's lunch break catching up, and talking about Maricruz and Sucre's daughter. Sucre informed them that he, Maricruz, and Lila were staying in town for a couple of months to enjoy some sunny weather, a nice break from the cold and windy weather of Chicago. They said their goodbyes, deciding that they would all meet for dinner that night and Sara went back to work. It was nice having Sucre back. In some ways it even made Sara feel closer to Michael.

**A/N: Hope you enjoyed chapter 12! I'm trying to write as often as I can and whenever I get spare moment. Sorry if I misled you with the chapter title...but you didn't actually think I would have Michael and Sara reunite without even some sort of climatic build up ;). Anyway I hope that despite my slow update rate I still have a few readers out there. Review to let me know if you're still reading! Much love.**


	13. Chapter 13: Now or Never

Ch. 13: Now or Never

It had been a month. One month since Mahone had arrived. One month since they had come up with the plan that was finally going to end the Company once and for all. Michael could not wait until he could finally be reunited with his family. It was all he truly wanted. Every month when the General would bring in a picture of Mikey, Michael would be overcome with a surplus of emotions. On one hand, he would feel so much joy and pride for the little miracle that he and Sara had created, but on the other he would feel an undeniable sense of rage because he couldn't be with his family. On top of all of this, he would also feel the deepest amount of disgust because the Company was able to get close enough to Mikey and Sara to get these pictures taken, without their knowing.

Michael's thoughts were interrupted by Mahone entering the room with a proud smile on his face and a piece of tape in hand. Today, Michael felt a glimmer of hope for the first time since Mahone first showed up.

"I'm assuming you got a good print?" Michael chuckled at the look of utter excitement on Mahone's face.

"Not only a fantastic print, but also from a guard who is dumber than a sack of bricks and slower than a tortoise. And look. I even already got his pass key." Mahone was so proud of himself, and Michael could tell.

"Good work Agent Mahone," Michael deadpanned. "Now bring that print over here."

Mahone complied and brought the piece of tape containing the guard's print to Michael. Michael took a deep breath and let it out. He was a nervous wreck. If this didn't work, he didn't know what else to try. If he couldn't copy this print, he didn't know if they were ever going to make it out of Company Headquarters alive. He poured the salt that he had requested because "his eggs were too bland" on the tape. He let it set before shaking off the excess salt that didn't stick to the tape. The purpose of the salt was to make the print three dimensional. Next, Michael took the bubble gum out of his mouth and pressed it to the three dimensional print. He took a deep breath. If this worked, they could escape. If this worked, he could return to his family. If this worked, he could get his life back. There was so much riding on this single piece of gum.

"Well, let's do this. It's now or never, and this is the first piece of gum that has remained intact. We've got to give it a shot, and since we have a pass key and a thumbprint, let's go," Michael said confidently. Mahone nodded and grabbed the backpack containing the final piece they needed for freedom.

He climbed on his bed and unscrewed the panel to the air vent. He climbed up and into the vent and motioned for Mahone to follow. Once they were both inside, they worked on screwing the vent panel back on to eliminate any possible leads as to how they could have escaped.

"C'mon. We better get moving. That curtain's only gonna stay closed for so long," Mahone reminded Michael.

On a normal day, there is a gaping window that allows the guards to watch Mahone and Michael 24/7. However today, Mahone requested that they drop a curtain over the window because they had made tremendous progress in creating something that could rebuild the Company overnight. The General reluctantly agreed and told them they had five hours between breakfast and lunch to finish whatever breakthrough they thought they had found.

Michael nodded understanding the urgency of the situation and led Mahone to the path to freedom. Over the past month, Mahone had walked from Michael's room to the only lab that was directly connected to the outside world. He counted the panels in the ceiling he would pass before making a turn and wrote this information down on a sheet of paper. Michael figured since they didn't have the blueprints of the place, they needed some sort of guide to get out. With the homemade blueprints in hand, Michael led Mahone forward 4 panels. They were officially over the hallway outside of Michael's room.

Many turns and panels later, Michael and Mahone arrived at the vent closest to the lab. Now since it was a lab, the only vents inside of it were ones connected to the outdoors to get rid of harmful fumes and chemicals. These vents were not connected to the rest of the building. To escape, Mahone and Michael would have to get inside the chemical lab, put on biohazard suits available in said lab, climb out through the fume hoods, and run like hell to make it out of there alive. This was it. This was their last chance at freedom, because if this didn't work…neither one of them wanted to think of the consequences.

"WAIT!" Michael frantically stopped.

"What?" Mahone questioned.

"We have to go back. We can't do this, we have to go back."

"You have got to be kidding me! I did not give up my life to come save you for you to give up when we are so close! I did not sacrifice my family for this!" Mahone angrily erupted.

"Don't you get it Alex? That's why we can't do this—because of our families. The Company has agents all over them. How do you think I've gotten all of those pictures of Mikey? We can't put them in danger. There has to be another way," Michael reasoned.

"That's why you didn't want to go through with this?" Mahone asked dumbfounded. "Oh man you had me worried there for a minute. I've got that part of the plan under control. My people have already taken care of that little problem. Now that your little outburst is over, can we just hurry up and get the hell out of here?" Mahone finished with a chuckle.

"Where would I be without you man?" Michael sighed relieved.

"Well probably rotting away in the Company Headquarters, but let's not think about that one. Now can we get on with this please?"

"Right."

Michael peeked through the vent in the ceiling to ensure that no guards or Company agents were in the hallway. This would prove to be the trickiest part of their escape. When he saw the hallway was all clear, Michael began to unscrew the ceiling panel. He dropped down to the floor, and motioned for Mahone to follow suit. While using Mahone's hand to give him a boost, Michael was able to cover the ceiling vent with the panel, once again to erase any trail of how they managed to escape.

"Do you have the gum?" Michael asked Mahone.

"Yes, it's right here," Mahone said handing over the gum.

"Here goes nothing."

Michael and Mahone held their breath as they waited to see if their "gum thumb" would work. They both let out a sigh of relief when they heard the activation sound and the door unlock. They opened the door and were about to get inside when they heard a voice that shocked them to their very core.

"Hello gentlemen. Just what do you think you're doing?"

**A/N: Sorry it's been so long since my last update. I've been super busy (and also somewhat discouraged based on the lack of reviews ;)). Please let me know if you're still interested, or if i need to just move on. Much love to those of you who have stuck with this story and are still reading. XOXO**


	14. Chapter 14: Now What?

**A/N: Wow I am officially the worst. I am so sorry I haven't update in forever! It took me so long to write this chapter because it is a super big turning point AND because I wanted it to be perfect. But that is no excuse. I'll try to get another update out within the week to make up for it. **

**A/N 2: I went ahead and continued on from where we left off, without going to Sara, Lincoln, and little Mike. We'll be back to them next chapter :). Anyway here is chapter 14. Hope y'all enjoy it!**

Ch. 14: Now What?

Michael and Mahone blankly stared back at the only person now standing in the way of their freedom. Before their very eyes stood the same man who had held them captive for all these months; the same man that had kept Michael from his son and wife; the General had won too many battles in the past few months, but today Michael and Mahone were going to win the war. They were going to get out of that hell-hole today, or they were going to die trying.

"Well? I'm waiting," the General smirked, almost amused by the whole situation.

Mahone looked over to Michael and for the first time since he had known Michael, Mahone was genuinely afraid that he did not have a plan. How could he? No one expected this to happen. The general never comes by the lab. The only person who is ever anywhere near the lab is the scrawny lab tech. What were the chances that the General just happened to be passing by the lab on the day of their planned escape?

Michael stared back at the General blankly. He was not afraid. Sure, he had a plan. It wasn't a very good plan, but it was a plan. All he could think of to do in a Hail Mary effort was to fight. The General didn't look that intimidating. Together, Michael believed that he and Mahone could incapacitate the General for long enough to escape. He looked to Mahone and instantly Mahone seemed to figure out what Michael was thinking. Mahone discretely nodded at Michael, a gesture that seemed to go unnoticed by the General.

"Well," Mahone began, "I was headed back to my room when I found Scofield here wandering through the halls. Luckily I caught him before he could do any damage to our company plans. He outsmarted me though, and tried to escape my clutches. I chased him all the way down here. He started rambling on and on about this door and how well designed and engineered it was. And that's about when you showed up."

The General stared blankly at Michael and Mahone and processed what Mahone had just told him.

"Well Scofield, do you have anything to say for yourself?" the General inquired.

"There is no explanation that you would understand for my actions, therefore I'm not even going to bother wasting my breath with an explanation I know you will ignore. Now, if it's all right with you gentlemen, I would like to return to my room now," Michael finished. He turned to Mahone and gave him the slightest of nods that would have gone undetected by any passerby. But for Mahone, it was just enough for him to pick up on and that's when it began.

Before the General could respond, Mahone had put him in a chokehold and was standing behind him. Michael reached into the General's pocket and grabbed the gun that he knew he would have. He pointed it at the General's chest.

"Give me one reason why I shouldn't blow your brains out right now," Michael threatened. "After everything you and your father have put me and my family through, give me one good reason why I shouldn't end your life right here, right now."

"Now now Mr. Scofield. Let's not do anything too rash. I'm sure we can talk this over like the mature adults that we are," the General tried to reason.

Unbeknownst to Michael and Mahone, the General had more control over the situation than they had thought. Before they knew it, the General kneed Mahone in the groin and knocked the gun from Michael's hand. Mahone doubled over in pain as Michael tried to recover the gun before the General could get a hold of it. However, Michael was unsuccessful and the General soon gained control of the situation. He backed up Michael and Mahone until their backs were against the wall and their hands were held up in a surrendered position.

Well now Michael was truly out of ideas. He knew he couldn't wrestle the General for the gun without the high chance that he or Mahone could be caught in the crossfire. Mahone, however, seemed to believe differently. He made a move toward the gun before kthe General stopped him.

"Ah ah ah. Just what do you think you're doing Mr. Mahone?" questioned the General. "Now," he continued, "how is it that you worded it? Give me one good reason why I shouldn't blow your brains out?"

_Stall. _That's the only solution Michael could think of. Maybe if he could distract the General for long enough, he or Mahone could come up with a plan to outsmart the General and regain control of the situation.

"You're bluffing," Mahone stated boldly.

"I beg your pardon?" responded the General appalled by Mahone's gutsy response.

"You heard me. You won't kill us – you can't. You need us. Without us, who's gonna help you rebuild your precious Company. Our minds can't be replaced and you know it. So tell me what you're actually gonna do to us?"

"You see, Mr. Mahone, that is where you are wrong," the General began. "Sure I cannot replace the magnificent mind of Mr. Scofield, but you on the other hand are…easily disposed of."

Michael's mind was scrambling. He knew what Mahone was doing. He knew that Mahone had expected him to have a plan, just like he always did, but this time was different. This time Michael's only plan was to stall; a plan that was quickly going to hell as a result of Mahone's overconfidence in Michael's capabilities. He was provoking the General in hopes of distracting him so that Michael could do whatever he needed to in order to regain control of the situation.

Michael was out of ideas and panicking when he saw the General point his gun at Mahone's chest. It was in this moment that Mahone too realized that Michael did not have a plan.

It was then that Mahone's mind began to scramble. _How could Michael Scofield be without a plan? How could this be happening? How were they going to get out of this one? Was this really the end of the road for him? _Sure, Michael and his brain were safe, but Mahone? That was another story. Mahone knew he didn't have anything to offer to convince the General to spare him. And Mahone wasn't afraid. If this was how it ended, he would be fine with it. Mahone knew that if he died in this moment, his life would have had some meaning.

And then it happened. Out of nowhere, the stranger who had been lurking in the shadows appeared. Except it wasn't a stranger at all. It was a face that Michael, Mahone, and even the General were all too familiar with.

At first Michael was afraid of the face that stood before him. He didn't know what to think. Was she here to help them or to hurt them? Before their very eyes stood none other than Gretchen Morgan.

Just as the General was about to turn around to see what (or rather who) had captured the attention of Mahone and Michael, Gretchen struck him on the head with the butt of her gun.

"Well hello gentlemen," she greeted. "Fancy seeing you here."

"What are you even doing here? You're supposed to be in prison," Michael questioned.

"Now, now, there will be time for all of those explanations later. Right now, we've got to escape. We only have so long before the General wakes up and sends the entire Company on a manhunt for us. Don't worry about your families. I have taken care of all of the guards that have been keeping tabs on them. But right now, I want to get out of here just as badly as you do, so I can see my daughter. Now c'mon let's move."

Without another word Michael and Mahone used the gum to open the lab and find their path to freedom. Once inside the lab, they found the vent that lead to the outside world, just as they planned to do, and climbed through the vent.

When they finally reached the outside world, Michael felt overwhelmed with emotion. They had done it. They escaped. He couldn't believe it.

Mahone's voice broke him from his thoughts. "Hey, remember when you said we would get a front row seat to watching the Company burn?" Mahone asked rhetorically. "When are you gonna get on that one."

"I thought you'd never ask," Michael answered triumphantly. He then pulled a remote from his pocket and pressed the single red button in the middle.

"Run!" Michael yelled. And that's when they began to run. They ran and they didn't look back until they heard the sound of a distant explosion. In the distance, Michael, Mahone, and Gretchen saw a distant glow.

"What is that?" Mahone asked.

"That," Michael panted out, "is the end of the Company."

**A/N: So there you have it. As always reviews are welcomed and loved! I'll try to get out the nect chapter soon! XOXO**


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